allensdk.brain_observatory.behavior.session_apis.abcs.session_base.behavior_ophys_base module

class allensdk.brain_observatory.behavior.session_apis.abcs.session_base.behavior_ophys_base.BehaviorOphysBase[source]

Bases: allensdk.brain_observatory.behavior.session_apis.abcs.session_base.behavior_base.BehaviorBase

Abstract base class implementing required methods for interacting with behavior + ophys session data.

Child classes should be instantiated with a fetch API that implements these methods.

get_average_projection(self) → allensdk.brain_observatory.behavior.image_api.Image[source]

Get an image whose values are the average obtained values at each pixel of the ophys movie over time.

Returns:
allensdk.brain_observatory.behavior.image_api.Image:

Array-like interface to avg projection image data and metadata.

get_cell_specimen_table(self) → pandas.core.frame.DataFrame[source]

Get a cell specimen dataframe containing ROI information about cells identified in an ophys experiment.

Returns:
pd.DataFrame

Cell ROI information organized into a dataframe. Index is the cell ROI IDs.

get_corrected_fluorescence_traces(self) → pandas.core.frame.DataFrame[source]

Get motion-corrected fluorescence traces.

Returns:
pd.DataFrame

Motion-corrected fluorescence traces organized into a dataframe. Index is the cell ROI IDs.

get_dff_traces(self) → pandas.core.frame.DataFrame[source]

Get a table of delta fluorescence over fluorescence traces.

Returns:
pd.DataFrame

The traces of dff (normalized fluorescence) organized into a dataframe. Index is the cell ROI IDs.

get_events(self) → pandas.core.frame.DataFrame[source]

Get event detection data

Returns:
pd.DataFrame
index:

cell_specimen_id: int

cell_roi_id: int events: np.array filtered_events: np.array lambdas: float64 noise_stds: float64

get_eye_tracking(self) → Union[pandas.core.frame.DataFrame, NoneType][source]

Get eye tracking data from behavior + ophys session.

Returns:
pd.DataFrame

A refined eye tracking dataframe that contains information about eye tracking ellipse fits, frame times, eye areas, pupil areas, and frames with likely blinks/outliers.

get_eye_tracking_rig_geometry(self) → dict[source]

Get eye tracking rig metadata from behavior + ophys session.

Returns:
dict

Includes geometry of monitor, camera, LED

get_max_projection(self) → allensdk.brain_observatory.behavior.image_api.Image[source]

Get an image whose values are the maximum obtained values at each pixel of the ophys movie over time.

Returns:
allensdk.brain_observatory.behavior.image_api.Image:

Array-like interface to max projection image data and metadata.

get_metadata(self) → Union[allensdk.brain_observatory.behavior.metadata.behavior_ophys_metadata.BehaviorOphysMetadata, dict][source]

Get behavior+ophys session metadata.

Returns:
dict if NWB
BehaviorOphysMetadata otherwise
get_motion_correction(self) → pandas.core.frame.DataFrame[source]

Get motion correction trace data.

Returns:
pd.DataFrame

A dataframe containing trace data used during motion correction computation.

get_ophys_experiment_id(self) → Union[int, NoneType][source]

Returns the ophys_experiment_id for the instantiated BehaviorOphys Session (or BehaviorOphys data fetcher) if applicable.

get_ophys_session_id(self) → Union[int, NoneType][source]

Returns the behavior + ophys_session_id associated with this experiment, if applicable.

get_ophys_timestamps(self) → numpy.ndarray[source]

Get optical physiology frame timestamps.

Returns:
np.ndarray

Timestamps associated with frames captured by the microscope.

get_stimulus_presentations(self) → pandas.core.frame.DataFrame[source]

Get stimulus presentation data.

NOTE: Uses monitor delay corrected stimulus timestamps.

Returns:
pd.DataFrame

Table whose rows are stimulus presentations (i.e. a given image, for a given duration, typically 250 ms) and whose columns are presentation characteristics.

get_stimulus_timestamps(self) → numpy.ndarray[source]

Get stimulus timestamps.

Returns:
np.ndarray

Timestamps associated with stimulus presentations on the monitor after accounting for monitor delay.